Add new plotPrecursorIons function and address issue #742

[jorainer]

In this PR:

• add new function plotPrecursorIons to visualize location of precursor ions in m/z - retention time plane.
• support exclusion of samples/groups from the definition of new features using the PeakDensity correspondence method (issue Support excluding samples for PeakDensity correspondence #742 ).

Unit tests and documentation included.

[jorainer]

@sneumann , I leave it up to you whether we want this small updates to be included in the upcoming release version or not...

[philouail]

All good to me ! really nice additions

[philouail]

Sorry @jorainer I just tested locally and realized something is wrong.

Can you also update the functions-Params.R document (line 239) to allow for NAs in sampleGroups ?

[jorainer]

good catch @philouail ! I've changed it now.

[jorainer]

Changed to draft because there seem to be some problems...

[jorainer]

OK, now we have also a fix for a bug that Phili spotted when testing the code (although the bug was not related to the present code).

[jorainer]

@sneumann , can you please have a look at this PR and eventually merge if you're OK?

[sneumann]

Looks good, thanks!
I haven't tested if there is any fallout if the PeakDensityParam() handling NAs in other downstream functions, like peak filling or plotting, is there any "worst-case" this could lead to unexpected/degenerate feature groups violating assumptions we take for granted ?
Yours, Steffen

[jorainer]

There shouldn't be any issue - no other function/method uses this parameter - and the PeakDensityParam() handles it well - so, should be all good, thanks.